Package picard.vcf
Enum GenotypeConcordanceStates.CallState
- java.lang.Object
-
- java.lang.Enum<GenotypeConcordanceStates.CallState>
-
- picard.vcf.GenotypeConcordanceStates.CallState
-
- All Implemented Interfaces:
Serializable
,Comparable<GenotypeConcordanceStates.CallState>
- Enclosing class:
- GenotypeConcordanceStates
public static enum GenotypeConcordanceStates.CallState extends Enum<GenotypeConcordanceStates.CallState>
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence. The Enum constants must be in the same order as the truth state to allow for comparison.
-
-
Enum Constant Summary
Enum Constants Enum Constant Description GT_FILTERED
HET_REF_VAR1
HET_REF_VAR2
HET_REF_VAR3
HET_VAR1_VAR2
HET_VAR1_VAR3
HET_VAR3_VAR4
HOM_REF
HOM_VAR1
HOM_VAR2
HOM_VAR3
IS_MIXED
LOW_DP
LOW_GQ
MISSING
NO_CALL
VC_FILTERED
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getCode()
static GenotypeConcordanceStates.CallState
getHet(int allele0idx, int allele1idx)
static GenotypeConcordanceStates.CallState
getHom(int alleleIdx)
static GenotypeConcordanceStates.CallState
valueOf(String name)
Returns the enum constant of this type with the specified name.static GenotypeConcordanceStates.CallState[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
-
-
-
Enum Constant Detail
-
MISSING
public static final GenotypeConcordanceStates.CallState MISSING
-
HOM_REF
public static final GenotypeConcordanceStates.CallState HOM_REF
-
HET_REF_VAR1
public static final GenotypeConcordanceStates.CallState HET_REF_VAR1
-
HET_VAR1_VAR2
public static final GenotypeConcordanceStates.CallState HET_VAR1_VAR2
-
HOM_VAR1
public static final GenotypeConcordanceStates.CallState HOM_VAR1
-
HET_REF_VAR2
public static final GenotypeConcordanceStates.CallState HET_REF_VAR2
-
HET_REF_VAR3
public static final GenotypeConcordanceStates.CallState HET_REF_VAR3
-
HET_VAR1_VAR3
public static final GenotypeConcordanceStates.CallState HET_VAR1_VAR3
-
HET_VAR3_VAR4
public static final GenotypeConcordanceStates.CallState HET_VAR3_VAR4
-
HOM_VAR2
public static final GenotypeConcordanceStates.CallState HOM_VAR2
-
HOM_VAR3
public static final GenotypeConcordanceStates.CallState HOM_VAR3
-
NO_CALL
public static final GenotypeConcordanceStates.CallState NO_CALL
-
LOW_GQ
public static final GenotypeConcordanceStates.CallState LOW_GQ
-
LOW_DP
public static final GenotypeConcordanceStates.CallState LOW_DP
-
VC_FILTERED
public static final GenotypeConcordanceStates.CallState VC_FILTERED
-
GT_FILTERED
public static final GenotypeConcordanceStates.CallState GT_FILTERED
-
IS_MIXED
public static final GenotypeConcordanceStates.CallState IS_MIXED
-
-
Method Detail
-
values
public static GenotypeConcordanceStates.CallState[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (GenotypeConcordanceStates.CallState c : GenotypeConcordanceStates.CallState.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
-
valueOf
public static GenotypeConcordanceStates.CallState valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
-
getHom
public static GenotypeConcordanceStates.CallState getHom(int alleleIdx)
-
getHet
public static GenotypeConcordanceStates.CallState getHet(int allele0idx, int allele1idx)
-
getCode
public int getCode()
-
-